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added support for Copasi Optimisation task. This also uses the -e option.
bugfix: added is_package_installed.r to MANIFEST.ini.
SBpipe v4.18.0, sbpiper v1.8.0, sbpipe_snake v1.0.0 and above are released under MIT License.
Previous versions of these packages were released under GNU GPL v3.
Added script for moving data sets and update indexes.
Project and documentation clean-up.
SBpipe is now available on pypi.org.
Improved setup.py file for python packaging
SBpipe tests no longer require CopasiSE.
Documentation update.
Added generate_tarball option to all the remaining pipelines in native SBpipe.
Improved output messages.
Added progress information for native SBpipe.
Added PCA analysis for the best parameter estimates. Replaced conda channel "r" with "conda-forge".
Improved data analysis scalability for parameter estimation (using Snakemake).
Added checks whether a COPASI model can be loaded and executed correctly. This is based on Python bindings for COPASI.
Optimisation of snakemake pipelines. Improved efficiency of rules for analyses.
Bugfix - SGE and LSF job names now include a random string, avoiding potential interactions among multiple
SBpipe executions. Whilst this does not affect the results, it was still a performance-related bug.
SBpipe R code is now an independent R package called sbpiper. This is imported by SBpipe as
an external dependency. Users can invoke SBpipe functions for data analysis directly from their R code.